Showing : genomicfeatures • reset
3
votes
8
replies
416
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 22 hours ago by ★ 3.4k • written 3 days ago by ▴ 20
0
votes
3
replies
274
views
How to get The evolutionary conservation scores for lncRNAs by the phastCons100way.UCSC.hg38 (3.7.1) R package
txdbmaker GenomicScores phastCons100way.UCSC.hg38 GenomicFeatures
5 weeks ago • updated 4 weeks ago rania.alanany • 0
3
votes
3
replies
398
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
12 weeks ago • updated 2 days ago mat149 ▴ 80
0
votes
1
reply
587
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 10 months ago by 67k • written 10 months ago by ▴ 10
2
votes
1
reply
879
views
Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 12 months ago by 67k • written 12 months ago by • 0
0
votes
1
reply
818
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
14 months ago rohitsatyam102 ▴ 20
2
votes
3
replies
3.4k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 15 months ago by 52k • written 15 months ago by • 0
2
votes
2
replies
741
views
Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
16 months ago Geert ▴ 10
0
votes
2
replies
1.4k
views
What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
18 months ago gernophil • 0
1
vote
4
replies
1.0k
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 18 months ago by 16k • written 19 months ago by • 0
1
vote
0
replies
663
views
Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
20 months ago Shreyash ▴ 10
4
votes
8
replies
2.1k
views
TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
MetID TxDB.Hsapiens.UCSC.hg38.knownGene locateVariants GenomicFeatures VariantAnnotation
21 months ago davidhillis • 0
0
votes
2
replies
1.2k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 23 months ago by • 0
0
votes
5
replies
1.6k
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 2.0 years ago by 67k • written 2.0 years ago by • 0
0
votes
0
replies
619
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
2.2 years ago nattzy94 ▴ 20
0
votes
2
replies
1.4k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 10
0
votes
4
replies
2.6k
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
5
votes
9
replies
1.9k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 2.4 years ago by 43k • written 2.7 years ago by • 0
0
votes
18
replies
4.4k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
2.9 years ago • updated 2.8 years ago rbenel ▴ 40
3
votes
3
replies
1.8k
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 2.6 years ago by 67k • written 3.0 years ago by ▴ 30
1
vote
2
replies
1.6k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
3.1 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.2k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.1 years ago by 16k • written 3.1 years ago by • 0
1
vote
2
replies
1.3k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.1 years ago Madza Farias-Virgens • 0
2
votes
2
replies
1.1k
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 3.1 years ago by 16k • written 3.1 years ago by • 0
5
votes
2
replies
1.3k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
3.3 years ago Pratik Mehta ▴ 10
0
votes
1
reply
1.4k
views
install GenomicFeatures fail
GenomicFeatures install
updated 3.3 years ago by 67k • written 3.3 years ago by ▴ 80
1
vote
4
replies
1.8k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
3.4 years ago A.J. ▴ 20
1
vote
3
replies
1.4k
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
3.4 years ago A.J. ▴ 20
1
vote
0
replies
1.3k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.4 years ago Matthias Munz ▴ 20
0
votes
0
replies
980
views
annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
3.7 years ago António Miguel de Jesus Domingues ▴ 510
0
votes
5
replies
3.3k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.7 years ago sieminsk • 0
2
votes
2
replies
2.0k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
3.8 years ago erhoppe • 0
0
votes
6
replies
1.5k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
3.9 years ago rproendo ▴ 30
0
votes
3
replies
1.4k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 3.1 years ago by • 0 • written 4.1 years ago by ▴ 120
0
votes
2
replies
3.6k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
votes
1
reply
830
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 3.9 years ago by ▴ 80 • written 4.2 years ago by ▴ 10
0
votes
1
reply
5.2k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 4.3 years ago by 67k • written 4.4 years ago by ▴ 90
3
votes
7
replies
1.8k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 4.4 years ago by 67k • written 4.4 years ago by ▴ 30
0
votes
1
reply
1.5k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 4.4 years ago by 4.1k • written 4.4 years ago by • 0
3
votes
6
replies
2.5k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 4.4 years ago by 25k • written 4.4 years ago by ▴ 120
0
votes
1
reply
1.5k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 4.6 years ago by 67k • written 4.6 years ago by ▴ 100
0
votes
2
replies
1.2k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 4.6 years ago by ★ 11k • written 4.6 years ago by ▴ 10
0
votes
0
replies
1.1k
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
4.6 years ago Guandong Shang ▴ 40
0
votes
2
replies
988
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 4.7 years ago by 67k • written 4.7 years ago by ▴ 40
2
votes
3
replies
2.1k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 4.7 years ago by 67k • written 4.7 years ago by ▴ 100
3
votes
4
replies
1.3k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 4.7 years ago by 16k • written 4.8 years ago by ▴ 40
1
vote
2
replies
1.1k
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 40
0
votes
0
replies
1.2k
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 4.8 years ago by 4.1k • written 4.8 years ago by • 0
0
votes
2
replies
1.1k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 4.9 years ago by 67k • written 4.9 years ago by • 0
8
votes
12
replies
6.2k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.4 years ago by • 0 • written 9.8 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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